This study aimed to assess the impact of genotype, location, and type of cultivation (organic) on the nutrient and anti-nutrient components of seven large-seeded bean (Phaseolus vulgaris L.) populations. All genotypes were cultivated during 2014 and 2015 in randomized complete block (RCB) experimental designs in three areas of the Prespa region (Pili, Patoulidio, Agios Germanos) in Greece. Particularly, total protein (18.79–23.93%), fiber (7.77–12%), starch (40.14–55.26%), and fat (1.84–2.58%) contents were analyzed and showed significant differences. In order to assess mineral content, firstly, the total ash percentage (4.31% to 5.20%) and secondly, trace elements and heavy metals were determined. The concentrations of identified inorganic metals showed large variations. The total phenolic content of the samples varied from 0.18 to 0.29 mg/g gallic acid equivalent (GAE). A major limitation of increasing the use of grain legumes as feed is the presence of diverse compounds in their grain, commonly referred to as antinutritional factors, and these are mainly trypsin inhibitors. Trypsin inhibitor levels were evaluated, with results varying from 21.8 to 138.5 TIU/g. Pili 2014 and 2015 were differently associated regarding the year of cultivation. Pili 2015 location was also very closely associated with the Patoulidio region, whereas Agios Germanos and Pili 2014 were the most different in terms of nutritional and antinutritional content.